[INFO   ] Starting gmx_MMPBSA v1.5.2
[DEBUG  ] WDIR          : /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs2/5ocx-rs2-free-energy/free-energy-312k
[DEBUG  ] AMBERHOME     : /home/romi/anaconda3/envs/gmxMMPBSA
[DEBUG  ] PYTHON EXE    : /home/romi/anaconda3/envs/gmxMMPBSA/bin/python
[DEBUG  ] PYTHON VERSION: 3.9.12 (main, Apr  5 2022, 06:56:58) [GCC 7.5.0]
[DEBUG  ] MPI           : /home/romi/anaconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG  ] ParmEd        : 3.4.3
[DEBUG  ] OS PLATFORM   : Linux-5.15.0-58-generic-x86_64-with-glibc2.31
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #64~20.04.1-Ubuntu SMP Fri Jan 6 16:42:31 UTC 2023
[DEBUG  ] OS PROCESSOR  : x86_64

[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 18 19 -ct dynamic-nopbc.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[DEBUG  ] |Input file:
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] |Input file generated by gmx_MMPBSA (v1.5.2)
[DEBUG  ] |Be careful with the variables you modify, some can have severe consequences on the results you obtain.
[DEBUG  ] |
[DEBUG  ] |# General namelist variables
[DEBUG  ] |&general
[DEBUG  ] |  sys_name             = ""                                             # System name
[DEBUG  ] |  startframe           = 10                                             # First frame to analyze
[DEBUG  ] |  endframe             = 9900                                       # Last frame to analyze
[DEBUG  ] |  interval             = 1600                                         # Number of frames between adjacent frames analyzed
[DEBUG  ] |  forcefields          = "oldff/leaprc.ff99SB,leaprc.gaff"              # Define the force field to build the Amber topology
[DEBUG  ] |  ions_parameters      = 1                                              # Define ions parameters to build the Amber topology
[DEBUG  ] |  PBRadii              = 3                                              # Define PBRadii to build amber topology from GROMACS files
[DEBUG  ] |  temperature          = 312                                        # Temperature
[DEBUG  ] |  qh_entropy           = 0                                              # Do quasi-harmonic calculation
[DEBUG  ] |  interaction_entropy  = 0                                              # Do Interaction Entropy calculation
[DEBUG  ] |  ie_segment           = 25                                             # Trajectory segment to calculate interaction entropy
[DEBUG  ] |  c2_entropy           = 0                                              # Do C2 Entropy calculation
[DEBUG  ] |  assign_chainID       = 0                                              # Assign chains ID
[DEBUG  ] |  exp_ki               = 0.0                                            # Experimental Ki in nM
[DEBUG  ] |  full_traj            = 0                                              # Print a full traj. AND the thread trajectories
[DEBUG  ] |  gmx_path             = ""                                             # Force to use this path to get GROMACS executable
[DEBUG  ] |  keep_files           = 2                                              # How many files to keep after successful completion
[DEBUG  ] |  netcdf               = 0                                              # Use NetCDF intermediate trajectories
[DEBUG  ] |  solvated_trajectory  = 1                                              # Define if it is necessary to cleanup the trajectories
[DEBUG  ] |  verbose              = 1                                              # How many energy terms to print in the final output
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# (AMBER) Generalized-Born namelist variables
[DEBUG  ] |&gb
[DEBUG  ] |  igb                  = 5                                              # GB model to use
[DEBUG  ] |  intdiel              = 1.0                                            # Internal dielectric constant for sander
[DEBUG  ] |  extdiel              = 78.5                                           # External dielectric constant for sander
[DEBUG  ] |  saltcon              = 0.0                                            # Salt concentration (M)
[DEBUG  ] |  surften              = 0.0072                                         # Surface tension
[DEBUG  ] |  surfoff              = 0.0                                            # Surface tension offset
[DEBUG  ] |  molsurf              = 0                                              # Use Connelly surface ('molsurf' program)
[DEBUG  ] |  msoffset             = 0.0                                            # Offset for molsurf calculation
[DEBUG  ] |  probe                = 1.4                                            # Solvent probe radius for surface area calc
[DEBUG  ] |  ifqnt                = 0                                              # Use QM on part of the system
[DEBUG  ] |  qm_theory            = ""                                             # Semi-empirical QM theory to use
[DEBUG  ] |  qm_residues          = ""                                             # Residues to treat with QM
[DEBUG  ] |  qmcharge_com         = 0                                              # Charge of QM region in complex
[DEBUG  ] |  qmcharge_lig         = 0                                              # Charge of QM region in ligand
[DEBUG  ] |  qmcharge_rec         = 0                                              # Charge of QM region in receptor
[DEBUG  ] |  qmcut                = 9999.0                                         # Cutoff in the QM region
[DEBUG  ] |  scfconv              = 1e-08                                          # Convergence criteria for the SCF calculation, in kcal/mol
[DEBUG  ] |  peptide_corr         = 0                                              # Apply MM correction to peptide linkages
[DEBUG  ] |  writepdb             = 1                                              # Write a PDB file of the selected QM region
[DEBUG  ] |  verbosity            = 0                                              # Controls the verbosity of QM/MM related output
[DEBUG  ] |  alpb                 = 0                                              # Use Analytical Linearized Poisson-Boltzmann (ALPB)
[DEBUG  ] |  arad_method          = 1                                              # Selected method to estimate the effective electrostatic size
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# (AMBER) Possion-Boltzmann namelist variables
[DEBUG  ] |&pb
[DEBUG  ] |  ipb                  = 2                                              # Dielectric model for PB
[DEBUG  ] |  inp                  = 2                                              # Nonpolar solvation method
[DEBUG  ] |  sander_apbs          = 0                                              # Use sander.APBS?
[DEBUG  ] |  indi                 = 1.0                                            # Internal dielectric constant
[DEBUG  ] |  exdi                 = 80.0                                           # External dielectric constant
[DEBUG  ] |  emem                 = 4.0                                            # Membrane dielectric constant
[DEBUG  ] |  smoothopt            = 1                                              # Set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary
[DEBUG  ] |  istrng               = 0.0                                            # Ionic strength (M)
[DEBUG  ] |  radiopt              = 1                                              # Use optimized radii?
[DEBUG  ] |  prbrad               = 1.4                                            # Probe radius
[DEBUG  ] |  iprob                = 2.0                                            # Mobile ion probe radius (Angstroms) for ion accessible surface used to define the Stern layer
[DEBUG  ] |  sasopt               = 0                                              # Molecular surface in PB implict model
[DEBUG  ] |  arcres               = 0.25                                           # The resolution (Å) to compute solvent accessible arcs
[DEBUG  ] |  memopt               = 0                                              # Use PB optimization for membrane
[DEBUG  ] |  mprob                = 2.7                                            # Membrane probe radius in Å
[DEBUG  ] |  mthick               = 40.0                                           # Membrane thickness
[DEBUG  ] |  mctrdz               = 0.0                                            # Distance to offset membrane in Z direction
[DEBUG  ] |  poretype             = 1                                              # Use exclusion region for channel proteins
[DEBUG  ] |  npbopt               = 0                                              # Use NonLinear PB solver?
[DEBUG  ] |  solvopt              = 1                                              # Select iterative solver
[DEBUG  ] |  accept               = 0.001                                          # Sets the iteration convergence criterion (relative to the initial residue)
[DEBUG  ] |  linit                = 1000                                           # Number of SCF iterations
[DEBUG  ] |  fillratio            = 4.0                                            # Ratio between the longest dimension of the rectangular finite-difference grid and that of the solute
[DEBUG  ] |  scale                = 2.0                                            # 1/scale = grid spacing for the finite difference solver (default = 1/2 Å)
[DEBUG  ] |  nbuffer              = 0.0                                            # Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface
[DEBUG  ] |  nfocus               = 2                                              # Electrostatic focusing calculation
[DEBUG  ] |  fscale               = 8                                              # Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation
[DEBUG  ] |  npbgrid              = 1                                              # Sets how often the finite-difference grid is regenerated
[DEBUG  ] |  bcopt                = 5                                              # Boundary condition option
[DEBUG  ] |  eneopt               = 2                                              # Compute electrostatic energy and forces
[DEBUG  ] |  frcopt               = 0                                              # Output for computing electrostatic forces
[DEBUG  ] |  scalec               = 0                                              # Option to compute reaction field energy and forces
[DEBUG  ] |  cutfd                = 5.0                                            # Cutoff for finite-difference interactions
[DEBUG  ] |  cutnb                = 0.0                                            # Cutoff for nonbonded interations
[DEBUG  ] |  nsnba                = 1                                              # Sets how often atom-based pairlist is generated
[DEBUG  ] |  decompopt            = 2                                              # Option to select different decomposition schemes when INP = 2
[DEBUG  ] |  use_rmin             = 1                                              # The option to set up van der Waals radii
[DEBUG  ] |  sprob                = 0.557                                          # Solvent probe radius for SASA used to compute the dispersion term
[DEBUG  ] |  vprob                = 1.3                                            # Solvent probe radius for molecular volume (the volume enclosed by SASA)
[DEBUG  ] |  rhow_effect          = 1.129                                          # Effective water density used in the non-polar dispersion term calculation
[DEBUG  ] |  use_sav              = 1                                              # Use molecular volume (the volume enclosed by SASA) for cavity term calculation
[DEBUG  ] |  cavity_surften       = 0.0378                                         # Surface tension
[DEBUG  ] |  cavity_offset        = -0.5692                                        # Offset for nonpolar solvation calc
[DEBUG  ] |  maxsph               = 400                                            # Approximate number of dots to represent the maximum atomic solvent accessible surface
[DEBUG  ] |  maxarcdot            = 1500                                           # Number of dots used to store arc dots per atom
[DEBUG  ] |  npbverb              = 0                                              # Option to turn on verbose mode
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# Decomposition namelist variables
[DEBUG  ] |&decomposition
[DEBUG  ] |  idecomp              = 1                                              # Which type of decomposition analysis to do
[DEBUG  ] |  dec_verbose          = 0                                              # Control energy terms are printed to the output
[DEBUG  ] |  print_res            = "within 6"                                     # Which residues to print decomposition data for
[DEBUG  ] |  csv_format           = 1                                              # Write decomposition data in CSV format
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] 
[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[DEBUG  ] Running command: echo name 18 GMXMMPBSA_REC\n name 19 GMXMMPBSA_LIG\n  18 | 19\n q\n | /usr/local/gromacs/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
[DEBUG  ]                      :-) GROMACS - gmx make_ndx, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx make_ndx, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs2/5ocx-rs2-free-energy/free-energy-312k
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "You could give Aristotle a tutorial. And you could thrill him to the core of his being. Such is the privilege of living after Newton, Darwin, Einstein, Planck, Watson, Crick and their colleagues." (Richard Dawkins)
[DEBUG  ] 
[DEBUG  ] Going to read 1 old index file(s)
[DEBUG  ] Counted atom numbers up to 98020 in index file
[DEBUG  ] 
[DEBUG  ]   0 System              : 98020 atoms
[DEBUG  ]   1 Protein             :  6723 atoms
[DEBUG  ]   2 Protein-H           :  3420 atoms
[DEBUG  ]   3 C-alpha             :   456 atoms
[DEBUG  ]   4 Backbone            :  1368 atoms
[DEBUG  ]   5 MainChain           :  1821 atoms
[DEBUG  ]   6 MainChain+Cb        :  2238 atoms
[DEBUG  ]   7 MainChain+H         :  2250 atoms
[DEBUG  ]   8 SideChain           :  4473 atoms
[DEBUG  ]   9 SideChain-H         :  1599 atoms
[DEBUG  ]  10 Prot-Masses         :  6723 atoms
[DEBUG  ]  11 non-Protein         : 91297 atoms
[DEBUG  ]  12 Water               : 91296 atoms
[DEBUG  ]  13 SOL                 : 91296 atoms
[DEBUG  ]  14 non-Water           :  6724 atoms
[DEBUG  ]  15 Ion                 :     1 atoms
[DEBUG  ]  16 NA                  :     1 atoms
[DEBUG  ]  17 Water_and_ions      : 91297 atoms
[DEBUG  ]  18 Chain_A             :  6489 atoms
[DEBUG  ]  19 Chain_B             :   234 atoms
[DEBUG  ] 
[DEBUG  ]  nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
[DEBUG  ]  'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
[DEBUG  ]  't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
[DEBUG  ]  'r': residue              'res' nr         'chain' char
[DEBUG  ]  "name": group             'case': case sensitive           'q': save and quit
[DEBUG  ]  'ri': residue index
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] Copied index group 18 'GMXMMPBSA_REC'
[DEBUG  ] Copied index group 19 'GMXMMPBSA_LIG'
[DEBUG  ] Merged two groups with OR: 6489 234 -> 6723
[DEBUG  ] 
[DEBUG  ]  20 GMXMMPBSA_REC_GMXMMPBSA_LIG:  6723 atoms
[DEBUG  ] 
[DEBUG  ] > 
[INFO   ] Normal Complex: Saving group 18_19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG  ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs2/5ocx-rs2-free-energy/free-energy-312k
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 98020 elements
[DEBUG  ] Group     1 (        Protein) has  6723 elements
[DEBUG  ] Group     2 (      Protein-H) has  3420 elements
[DEBUG  ] Group     3 (        C-alpha) has   456 elements
[DEBUG  ] Group     4 (       Backbone) has  1368 elements
[DEBUG  ] Group     5 (      MainChain) has  1821 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  2238 elements
[DEBUG  ] Group     7 (    MainChain+H) has  2250 elements
[DEBUG  ] Group     8 (      SideChain) has  4473 elements
[DEBUG  ] Group     9 (    SideChain-H) has  1599 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  6723 elements
[DEBUG  ] Group    11 (    non-Protein) has 91297 elements
[DEBUG  ] Group    12 (          Water) has 91296 elements
[DEBUG  ] Group    13 (            SOL) has 91296 elements
[DEBUG  ] Group    14 (      non-Water) has  6724 elements
[DEBUG  ] Group    15 (            Ion) has     1 elements
[DEBUG  ] Group    16 (             NA) has     1 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 91297 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6489 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has   234 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  6723 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time   10.000   Reading frame       0 time    0.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time   10.000   
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "You could give Aristotle a tutorial. And you could thrill him to the core of his being. Such is the privilege of living after Newton, Darwin, Einstein, Planck, Watson, Crick and their colleagues." (Richard Dawkins)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 20: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group 18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG  ] Running command: echo 18 | /usr/local/gromacs/bin/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs2/5ocx-rs2-free-energy/free-energy-312k
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 98020 elements
[DEBUG  ] Group     1 (        Protein) has  6723 elements
[DEBUG  ] Group     2 (      Protein-H) has  3420 elements
[DEBUG  ] Group     3 (        C-alpha) has   456 elements
[DEBUG  ] Group     4 (       Backbone) has  1368 elements
[DEBUG  ] Group     5 (      MainChain) has  1821 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  2238 elements
[DEBUG  ] Group     7 (    MainChain+H) has  2250 elements
[DEBUG  ] Group     8 (      SideChain) has  4473 elements
[DEBUG  ] Group     9 (    SideChain-H) has  1599 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  6723 elements
[DEBUG  ] Group    11 (    non-Protein) has 91297 elements
[DEBUG  ] Group    12 (          Water) has 91296 elements
[DEBUG  ] Group    13 (            SOL) has 91296 elements
[DEBUG  ] Group    14 (      non-Water) has  6724 elements
[DEBUG  ] Group    15 (            Ion) has     1 elements
[DEBUG  ] Group    16 (             NA) has     1 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 91297 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6489 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has   234 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  6723 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time   10.000   Reading frame       0 time    0.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time   10.000   
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "You could give Aristotle a tutorial. And you could thrill him to the core of his being. Such is the privilege of living after Newton, Darwin, Einstein, Planck, Watson, Crick and their colleagues." (Richard Dawkins)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 18: 'GMXMMPBSA_REC'
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG  ] Running command: echo 19 | /usr/local/gromacs/bin/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs2/5ocx-rs2-free-energy/free-energy-312k
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 98020 elements
[DEBUG  ] Group     1 (        Protein) has  6723 elements
[DEBUG  ] Group     2 (      Protein-H) has  3420 elements
[DEBUG  ] Group     3 (        C-alpha) has   456 elements
[DEBUG  ] Group     4 (       Backbone) has  1368 elements
[DEBUG  ] Group     5 (      MainChain) has  1821 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  2238 elements
[DEBUG  ] Group     7 (    MainChain+H) has  2250 elements
[DEBUG  ] Group     8 (      SideChain) has  4473 elements
[DEBUG  ] Group     9 (    SideChain-H) has  1599 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  6723 elements
[DEBUG  ] Group    11 (    non-Protein) has 91297 elements
[DEBUG  ] Group    12 (          Water) has 91296 elements
[DEBUG  ] Group    13 (            SOL) has 91296 elements
[DEBUG  ] Group    14 (      non-Water) has  6724 elements
[DEBUG  ] Group    15 (            Ion) has     1 elements
[DEBUG  ] Group    16 (             NA) has     1 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 91297 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6489 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has   234 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  6723 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time   10.000   Reading frame       0 time    0.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time   10.000   
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "You could give Aristotle a tutorial. And you could thrill him to the core of his being. Such is the privilege of living after Newton, Darwin, Einstein, Planck, Watson, Crick and their colleagues." (Richard Dawkins)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 19: 'GMXMMPBSA_LIG'
[INFO   ] Checking the structures consistency...
[INFO   ] 
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
[INFO   ] Detected CHARMM force field topology format...
[INFO   ] Assigning PBRadii mbondi2 to Complex...
[INFO   ] Writing Normal Complex AMBER topology...
[INFO   ] No Receptor topology file was defined. Using ST approach...
[INFO   ] Building AMBER Receptor topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Receptor...
[INFO   ] Writing Normal Receptor AMBER topology...
[INFO   ] No Ligand topology file was defined. Using ST approach...
[INFO   ] Building AMBER Ligand topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 52 residues:
R:A:LEU:29  R:A:ARG:30  R:A:SER:31  R:A:ALA:32  R:A:PHE:33  R:A:VAL:34  R:A:ASP:51  R:A:ASP:52  R:A:ASN:67  R:A:TRP:92
R:A:GLY:94  R:A:SER:97  R:A:PHE:99  R:A:CYS:217 R:B:SER:249 R:B:TYR:250 R:B:PHE:251 R:B:TRP:265 R:B:SER:268 R:B:ILE:270
R:B:HIS:271 R:B:THR:272 R:B:THR:274 R:B:TYR:276 R:B:ILE:316 R:B:ARG:317 R:B:GLY:318 R:B:GLY:319 R:B:SER:320 R:B:SER:321
R:B:ASN:322 R:B:ALA:349 R:B:PRO:350 R:B:GLY:351 R:B:CYS:352 R:B:GLY:353 R:B:ASP:354 R:B:TRP:412 R:B:PRO:436 R:B:ARG:437
L:B:PRO:438 L:C:GLY:442 L:C:GLU:443 L:C:GLU:444 L:C:GLY:445 L:C:LYS:446 L:C:ALA:447 L:C:GLY:448 L:C:ALA:449 L:C:ARG:450
L:C:GLY:451 L:C:GLU:452

[INFO   ] Cleaning normal complex trajectories...
[DEBUG  ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs2/5ocx-rs2-free-energy/free-energy-312k
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ] 
[DEBUG  ] Will write xtc: Compressed trajectory (portable xdr format): xtc
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 98020 elements
[DEBUG  ] Group     1 (        Protein) has  6723 elements
[DEBUG  ] Group     2 (      Protein-H) has  3420 elements
[DEBUG  ] Group     3 (        C-alpha) has   456 elements
[DEBUG  ] Group     4 (       Backbone) has  1368 elements
[DEBUG  ] Group     5 (      MainChain) has  1821 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  2238 elements
[DEBUG  ] Group     7 (    MainChain+H) has  2250 elements
[DEBUG  ] Group     8 (      SideChain) has  4473 elements
[DEBUG  ] Group     9 (    SideChain-H) has  1599 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  6723 elements
[DEBUG  ] Group    11 (    non-Protein) has 91297 elements
[DEBUG  ] Group    12 (          Water) has 91296 elements
[DEBUG  ] Group    13 (            SOL) has 91296 elements
[DEBUG  ] Group    14 (      non-Water) has  6724 elements
[DEBUG  ] Group    15 (            Ion) has     1 elements
[DEBUG  ] Group    16 (             NA) has     1 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 91297 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6489 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has   234 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  6723 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Using output precision of 0.001 (nm)
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time   10.000    ->  frame      1 time   10.000      Reading frame       2 time   20.000    ->  frame      2 time   20.000      Reading frame       3 time   30.000    ->  frame      3 time   30.000      Reading frame       4 time   40.000    ->  frame      4 time   40.000      Reading frame       5 time   50.000    ->  frame      5 time   50.000      Reading frame       6 time   60.000    ->  frame      6 time   60.000      Reading frame       7 time   70.000    ->  frame      7 time   70.000      Reading frame       8 time   80.000    ->  frame      8 time   80.000      Reading frame       9 time   90.000    ->  frame      9 time   90.000      Reading frame      10 time  100.000    ->  frame     10 time  100.000      Reading frame      11 time  110.000   Reading frame      12 time  120.000   Reading frame      13 time  130.000   Reading frame      14 time  140.000   Reading frame      15 time  150.000   Reading frame      16 time  160.000   Reading frame      17 time  170.000   Reading frame      18 time  180.000   Reading frame      19 time  190.000   Reading frame      20 time  200.000    ->  frame     20 time  200.000      Reading frame      30 time  300.000    ->  frame     30 time  300.000      Reading frame      40 time  400.000    ->  frame     40 time  400.000      Reading frame      50 time  500.000    ->  frame     50 time  500.000      Reading frame      60 time  600.000    ->  frame     60 time  600.000      Reading frame      70 time  700.000    ->  frame     70 time  700.000      Reading frame      80 time  800.000    ->  frame     80 time  800.000      Reading frame      90 time  900.000    ->  frame     90 time  900.000      Reading frame     100 time 1000.000    ->  frame    100 time 1000.000      Reading frame     110 time 1100.000    ->  frame    110 time 1100.000      Reading frame     120 time 1200.000    ->  frame    120 time 1200.000      Reading frame     130 time 1300.000    ->  frame    130 time 1300.000      Reading frame     140 time 1400.000    ->  frame    140 time 1400.000      Reading frame     150 time 1500.000    ->  frame    150 time 1500.000      Reading frame     160 time 1600.000    ->  frame    160 time 1600.000      Reading frame     170 time 1700.000    ->  frame    170 time 1700.000      Reading frame     180 time 1800.000    ->  frame    180 time 1800.000      Reading frame     190 time 1900.000    ->  frame    190 time 1900.000      Reading frame     200 time 2000.000    ->  frame    200 time 2000.000       ->  frame    210 time 2100.000       ->  frame    220 time 2200.000       ->  frame    230 time 2300.000       ->  frame    240 time 2400.000       ->  frame    250 time 2500.000       ->  frame    260 time 2600.000       ->  frame    270 time 2700.000       ->  frame    280 time 2800.000       ->  frame    290 time 2900.000      Reading frame     300 time 3000.000    ->  frame    300 time 3000.000       ->  frame    310 time 3100.000       ->  frame    320 time 3200.000       ->  frame    330 time 3300.000       ->  frame    340 time 3400.000       ->  frame    350 time 3500.000       ->  frame    360 time 3600.000       ->  frame    370 time 3700.000       ->  frame    380 time 3800.000       ->  frame    390 time 3900.000      Reading frame     400 time 4000.000    ->  frame    400 time 4000.000       ->  frame    410 time 4100.000       ->  frame    420 time 4200.000       ->  frame    430 time 4300.000       ->  frame    440 time 4400.000       ->  frame    450 time 4500.000       ->  frame    460 time 4600.000       ->  frame    470 time 4700.000       ->  frame    480 time 4800.000       ->  frame    490 time 4900.000      Reading frame     500 time 5000.000    ->  frame    500 time 5000.000       ->  frame    510 time 5100.000       ->  frame    520 time 5200.000       ->  frame    530 time 5300.000       ->  frame    540 time 5400.000       ->  frame    550 time 5500.000       ->  frame    560 time 5600.000       ->  frame    570 time 5700.000       ->  frame    580 time 5800.000       ->  frame    590 time 5900.000      Reading frame     600 time 6000.000    ->  frame    600 time 6000.000       ->  frame    610 time 6100.000       ->  frame    620 time 6200.000       ->  frame    630 time 6300.000       ->  frame    640 time 6400.000       ->  frame    650 time 6500.000       ->  frame    660 time 6600.000       ->  frame    670 time 6700.000       ->  frame    680 time 6800.000       ->  frame    690 time 6900.000      Reading frame     700 time 7000.000    ->  frame    700 time 7000.000       ->  frame    710 time 7100.000       ->  frame    720 time 7200.000       ->  frame    730 time 7300.000       ->  frame    740 time 7400.000       ->  frame    750 time 7500.000       ->  frame    760 time 7600.000       ->  frame    770 time 7700.000       ->  frame    780 time 7800.000       ->  frame    790 time 7900.000      Reading frame     800 time 8000.000    ->  frame    800 time 8000.000       ->  frame    810 time 8100.000       ->  frame    820 time 8200.000       ->  frame    830 time 8300.000       ->  frame    840 time 8400.000       ->  frame    850 time 8500.000       ->  frame    860 time 8600.000       ->  frame    870 time 8700.000       ->  frame    880 time 8800.000       ->  frame    890 time 8900.000      Reading frame     900 time 9000.000    ->  frame    900 time 9000.000       ->  frame    910 time 9100.000       ->  frame    920 time 9200.000       ->  frame    930 time 9300.000       ->  frame    940 time 9400.000       ->  frame    950 time 9500.000       ->  frame    960 time 9600.000       ->  frame    970 time 9700.000       ->  frame    980 time 9800.000       ->  frame    990 time 9900.000      Reading frame    1000 time 10000.000    ->  frame   1000 time 10000.000       ->  frame   1010 time 10100.000       ->  frame   1020 time 10200.000       ->  frame   1030 time 10300.000       ->  frame   1040 time 10400.000       ->  frame   1050 time 10500.000       ->  frame   1060 time 10600.000       ->  frame   1070 time 10700.000       ->  frame   1080 time 10800.000       ->  frame   1090 time 10900.000      Reading frame    1100 time 11000.000    ->  frame   1100 time 11000.000       ->  frame   1110 time 11100.000       ->  frame   1120 time 11200.000       ->  frame   1130 time 11300.000       ->  frame   1140 time 11400.000       ->  frame   1150 time 11500.000       ->  frame   1160 time 11600.000       ->  frame   1170 time 11700.000       ->  frame   1180 time 11800.000       ->  frame   1190 time 11900.000      Reading frame    1200 time 12000.000    ->  frame   1200 time 12000.000       ->  frame   1210 time 12100.000       ->  frame   1220 time 12200.000       ->  frame   1230 time 12300.000       ->  frame   1240 time 12400.000       ->  frame   1250 time 12500.000       ->  frame   1260 time 12600.000       ->  frame   1270 time 12700.000       ->  frame   1280 time 12800.000       ->  frame   1290 time 12900.000      Reading frame    1300 time 13000.000    ->  frame   1300 time 13000.000       ->  frame   1310 time 13100.000       ->  frame   1320 time 13200.000       ->  frame   1330 time 13300.000       ->  frame   1340 time 13400.000       ->  frame   1350 time 13500.000       ->  frame   1360 time 13600.000       ->  frame   1370 time 13700.000       ->  frame   1380 time 13800.000       ->  frame   1390 time 13900.000      Reading frame    1400 time 14000.000    ->  frame   1400 time 14000.000       ->  frame   1410 time 14100.000       ->  frame   1420 time 14200.000       ->  frame   1430 time 14300.000       ->  frame   1440 time 14400.000       ->  frame   1450 time 14500.000       ->  frame   1460 time 14600.000       ->  frame   1470 time 14700.000       ->  frame   1480 time 14800.000       ->  frame   1490 time 14900.000      Reading frame    1500 time 15000.000    ->  frame   1500 time 15000.000       ->  frame   1510 time 15100.000       ->  frame   1520 time 15200.000       ->  frame   1530 time 15300.000       ->  frame   1540 time 15400.000       ->  frame   1550 time 15500.000       ->  frame   1560 time 15600.000       ->  frame   1570 time 15700.000       ->  frame   1580 time 15800.000       ->  frame   1590 time 15900.000      Reading frame    1600 time 16000.000    ->  frame   1600 time 16000.000       ->  frame   1610 time 16100.000       ->  frame   1620 time 16200.000       ->  frame   1630 time 16300.000       ->  frame   1640 time 16400.000       ->  frame   1650 time 16500.000       ->  frame   1660 time 16600.000       ->  frame   1670 time 16700.000       ->  frame   1680 time 16800.000       ->  frame   1690 time 16900.000      Reading frame    1700 time 17000.000    ->  frame   1700 time 17000.000       ->  frame   1710 time 17100.000       ->  frame   1720 time 17200.000       ->  frame   1730 time 17300.000       ->  frame   1740 time 17400.000       ->  frame   1750 time 17500.000       ->  frame   1760 time 17600.000       ->  frame   1770 time 17700.000       ->  frame   1780 time 17800.000       ->  frame   1790 time 17900.000      Reading frame    1800 time 18000.000    ->  frame   1800 time 18000.000       ->  frame   1810 time 18100.000       ->  frame   1820 time 18200.000       ->  frame   1830 time 18300.000       ->  frame   1840 time 18400.000       ->  frame   1850 time 18500.000       ->  frame   1860 time 18600.000       ->  frame   1870 time 18700.000       ->  frame   1880 time 18800.000       ->  frame   1890 time 18900.000      Reading frame    1900 time 19000.000    ->  frame   1900 time 19000.000       ->  frame   1910 time 19100.000       ->  frame   1920 time 19200.000       ->  frame   1930 time 19300.000       ->  frame   1940 time 19400.000       ->  frame   1950 time 19500.000       ->  frame   1960 time 19600.000       ->  frame   1970 time 19700.000       ->  frame   1980 time 19800.000       ->  frame   1990 time 19900.000      Reading frame    2000 time 20000.000    ->  frame   2000 time 20000.000       ->  frame   2010 time 20100.000       ->  frame   2020 time 20200.000       ->  frame   2030 time 20300.000       ->  frame   2040 time 20400.000       ->  frame   2050 time 20500.000       ->  frame   2060 time 20600.000       ->  frame   2070 time 20700.000       ->  frame   2080 time 20800.000       ->  frame   2090 time 20900.000       ->  frame   2100 time 21000.000       ->  frame   2110 time 21100.000       ->  frame   2120 time 21200.000       ->  frame   2130 time 21300.000       ->  frame   2140 time 21400.000       ->  frame   2150 time 21500.000       ->  frame   2160 time 21600.000       ->  frame   2170 time 21700.000       ->  frame   2180 time 21800.000       ->  frame   2190 time 21900.000       ->  frame   2200 time 22000.000       ->  frame   2210 time 22100.000       ->  frame   2220 time 22200.000       ->  frame   2230 time 22300.000       ->  frame   2240 time 22400.000       ->  frame   2250 time 22500.000       ->  frame   2260 time 22600.000       ->  frame   2270 time 22700.000       ->  frame   2280 time 22800.000       ->  frame   2290 time 22900.000       ->  frame   2300 time 23000.000       ->  frame   2310 time 23100.000       ->  frame   2320 time 23200.000       ->  frame   2330 time 23300.000       ->  frame   2340 time 23400.000       ->  frame   2350 time 23500.000       ->  frame   2360 time 23600.000       ->  frame   2370 time 23700.000       ->  frame   2380 time 23800.000       ->  frame   2390 time 23900.000       ->  frame   2400 time 24000.000       ->  frame   2410 time 24100.000       ->  frame   2420 time 24200.000       ->  frame   2430 time 24300.000       ->  frame   2440 time 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frame   7240 time 72400.000       ->  frame   7250 time 72500.000       ->  frame   7260 time 72600.000       ->  frame   7270 time 72700.000       ->  frame   7280 time 72800.000       ->  frame   7290 time 72900.000       ->  frame   7300 time 73000.000       ->  frame   7310 time 73100.000       ->  frame   7320 time 73200.000       ->  frame   7330 time 73300.000       ->  frame   7340 time 73400.000       ->  frame   7350 time 73500.000       ->  frame   7360 time 73600.000       ->  frame   7370 time 73700.000       ->  frame   7380 time 73800.000       ->  frame   7390 time 73900.000       ->  frame   7400 time 74000.000       ->  frame   7410 time 74100.000       ->  frame   7420 time 74200.000       ->  frame   7430 time 74300.000       ->  frame   7440 time 74400.000       ->  frame   7450 time 74500.000       ->  frame   7460 time 74600.000       ->  frame   7470 time 74700.000       ->  frame   7480 time 74800.000       ->  frame   7490 time 74900.000       ->  frame   7500 time 75000.000       ->  frame   7510 time 75100.000       ->  frame   7520 time 75200.000       ->  frame   7530 time 75300.000       ->  frame   7540 time 75400.000       ->  frame   7550 time 75500.000       ->  frame   7560 time 75600.000       ->  frame   7570 time 75700.000       ->  frame   7580 time 75800.000       ->  frame   7590 time 75900.000       ->  frame   7600 time 76000.000       ->  frame   7610 time 76100.000       ->  frame   7620 time 76200.000       ->  frame   7630 time 76300.000       ->  frame   7640 time 76400.000       ->  frame   7650 time 76500.000       ->  frame   7660 time 76600.000       ->  frame   7670 time 76700.000       ->  frame   7680 time 76800.000       ->  frame   7690 time 76900.000       ->  frame   7700 time 77000.000       ->  frame   7710 time 77100.000       ->  frame   7720 time 77200.000       ->  frame   7730 time 77300.000       ->  frame   7740 time 77400.000       ->  frame   7750 time 77500.000       ->  frame   7760 time 77600.000       ->  frame   7770 time 77700.000       ->  frame   7780 time 77800.000       ->  frame   7790 time 77900.000       ->  frame   7800 time 78000.000       ->  frame   7810 time 78100.000       ->  frame   7820 time 78200.000       ->  frame   7830 time 78300.000       ->  frame   7840 time 78400.000       ->  frame   7850 time 78500.000       ->  frame   7860 time 78600.000       ->  frame   7870 time 78700.000       ->  frame   7880 time 78800.000       ->  frame   7890 time 78900.000       ->  frame   7900 time 79000.000       ->  frame   7910 time 79100.000       ->  frame   7920 time 79200.000       ->  frame   7930 time 79300.000       ->  frame   7940 time 79400.000       ->  frame   7950 time 79500.000       ->  frame   7960 time 79600.000       ->  frame   7970 time 79700.000       ->  frame   7980 time 79800.000       ->  frame   7990 time 79900.000      Reading frame    8000 time 80000.000    ->  frame   8000 time 80000.000       ->  frame   8010 time 80100.000       ->  frame   8020 time 80200.000       ->  frame   8030 time 80300.000       ->  frame   8040 time 80400.000       ->  frame   8050 time 80500.000       ->  frame   8060 time 80600.000       ->  frame   8070 time 80700.000       ->  frame   8080 time 80800.000       ->  frame   8090 time 80900.000       ->  frame   8100 time 81000.000       ->  frame   8110 time 81100.000       ->  frame   8120 time 81200.000       ->  frame   8130 time 81300.000       ->  frame   8140 time 81400.000       ->  frame   8150 time 81500.000       ->  frame   8160 time 81600.000       ->  frame   8170 time 81700.000       ->  frame   8180 time 81800.000       ->  frame   8190 time 81900.000       ->  frame   8200 time 82000.000       ->  frame   8210 time 82100.000       ->  frame   8220 time 82200.000       ->  frame   8230 time 82300.000       ->  frame   8240 time 82400.000       ->  frame   8250 time 82500.000       ->  frame   8260 time 82600.000       ->  frame   8270 time 82700.000       ->  frame   8280 time 82800.000       ->  frame   8290 time 82900.000       ->  frame   8300 time 83000.000       ->  frame   8310 time 83100.000       ->  frame   8320 time 83200.000       ->  frame   8330 time 83300.000       ->  frame   8340 time 83400.000       ->  frame   8350 time 83500.000       ->  frame   8360 time 83600.000       ->  frame   8370 time 83700.000       ->  frame   8380 time 83800.000       ->  frame   8390 time 83900.000       ->  frame   8400 time 84000.000       ->  frame   8410 time 84100.000       ->  frame   8420 time 84200.000       ->  frame   8430 time 84300.000       ->  frame   8440 time 84400.000       ->  frame   8450 time 84500.000       ->  frame   8460 time 84600.000       ->  frame   8470 time 84700.000       ->  frame   8480 time 84800.000       ->  frame   8490 time 84900.000       ->  frame   8500 time 85000.000       ->  frame   8510 time 85100.000       ->  frame   8520 time 85200.000       ->  frame   8530 time 85300.000       ->  frame   8540 time 85400.000       ->  frame   8550 time 85500.000       ->  frame   8560 time 85600.000       ->  frame   8570 time 85700.000       ->  frame   8580 time 85800.000       ->  frame   8590 time 85900.000       ->  frame   8600 time 86000.000       ->  frame   8610 time 86100.000       ->  frame   8620 time 86200.000       ->  frame   8630 time 86300.000       ->  frame   8640 time 86400.000       ->  frame   8650 time 86500.000       ->  frame   8660 time 86600.000       ->  frame   8670 time 86700.000       ->  frame   8680 time 86800.000       ->  frame   8690 time 86900.000       ->  frame   8700 time 87000.000       ->  frame   8710 time 87100.000       ->  frame   8720 time 87200.000       ->  frame   8730 time 87300.000       ->  frame   8740 time 87400.000       ->  frame   8750 time 87500.000       ->  frame   8760 time 87600.000       ->  frame   8770 time 87700.000       ->  frame   8780 time 87800.000       ->  frame   8790 time 87900.000       ->  frame   8800 time 88000.000       ->  frame   8810 time 88100.000       ->  frame   8820 time 88200.000       ->  frame   8830 time 88300.000       ->  frame   8840 time 88400.000       ->  frame   8850 time 88500.000       ->  frame   8860 time 88600.000       ->  frame   8870 time 88700.000       ->  frame   8880 time 88800.000       ->  frame   8890 time 88900.000       ->  frame   8900 time 89000.000       ->  frame   8910 time 89100.000       ->  frame   8920 time 89200.000       ->  frame   8930 time 89300.000       ->  frame   8940 time 89400.000       ->  frame   8950 time 89500.000       ->  frame   8960 time 89600.000       ->  frame   8970 time 89700.000       ->  frame   8980 time 89800.000       ->  frame   8990 time 89900.000      Reading frame    9000 time 90000.000    ->  frame   9000 time 90000.000       ->  frame   9010 time 90100.000       ->  frame   9020 time 90200.000       ->  frame   9030 time 90300.000       ->  frame   9040 time 90400.000       ->  frame   9050 time 90500.000       ->  frame   9060 time 90600.000       ->  frame   9070 time 90700.000       ->  frame   9080 time 90800.000       ->  frame   9090 time 90900.000       ->  frame   9100 time 91000.000       ->  frame   9110 time 91100.000       ->  frame   9120 time 91200.000       ->  frame   9130 time 91300.000       ->  frame   9140 time 91400.000       ->  frame   9150 time 91500.000       ->  frame   9160 time 91600.000       ->  frame   9170 time 91700.000       ->  frame   9180 time 91800.000       ->  frame   9190 time 91900.000       ->  frame   9200 time 92000.000       ->  frame   9210 time 92100.000       ->  frame   9220 time 92200.000       ->  frame   9230 time 92300.000       ->  frame   9240 time 92400.000       ->  frame   9250 time 92500.000       ->  frame   9260 time 92600.000       ->  frame   9270 time 92700.000       ->  frame   9280 time 92800.000       ->  frame   9290 time 92900.000       ->  frame   9300 time 93000.000       ->  frame   9310 time 93100.000       ->  frame   9320 time 93200.000       ->  frame   9330 time 93300.000       ->  frame   9340 time 93400.000       ->  frame   9350 time 93500.000       ->  frame   9360 time 93600.000       ->  frame   9370 time 93700.000       ->  frame   9380 time 93800.000       ->  frame   9390 time 93900.000       ->  frame   9400 time 94000.000       ->  frame   9410 time 94100.000       ->  frame   9420 time 94200.000       ->  frame   9430 time 94300.000       ->  frame   9440 time 94400.000       ->  frame   9450 time 94500.000       ->  frame   9460 time 94600.000       ->  frame   9470 time 94700.000       ->  frame   9480 time 94800.000       ->  frame   9490 time 94900.000       ->  frame   9500 time 95000.000       ->  frame   9510 time 95100.000       ->  frame   9520 time 95200.000       ->  frame   9530 time 95300.000       ->  frame   9540 time 95400.000       ->  frame   9550 time 95500.000       ->  frame   9560 time 95600.000       ->  frame   9570 time 95700.000       ->  frame   9580 time 95800.000       ->  frame   9590 time 95900.000       ->  frame   9600 time 96000.000       ->  frame   9610 time 96100.000       ->  frame   9620 time 96200.000       ->  frame   9630 time 96300.000       ->  frame   9640 time 96400.000       ->  frame   9650 time 96500.000       ->  frame   9660 time 96600.000       ->  frame   9670 time 96700.000       ->  frame   9680 time 96800.000       ->  frame   9690 time 96900.000       ->  frame   9700 time 97000.000       ->  frame   9710 time 97100.000       ->  frame   9720 time 97200.000       ->  frame   9730 time 97300.000       ->  frame   9740 time 97400.000       ->  frame   9750 time 97500.000       ->  frame   9760 time 97600.000       ->  frame   9770 time 97700.000       ->  frame   9780 time 97800.000       ->  frame   9790 time 97900.000       ->  frame   9800 time 98000.000       ->  frame   9810 time 98100.000       ->  frame   9820 time 98200.000       ->  frame   9830 time 98300.000       ->  frame   9840 time 98400.000       ->  frame   9850 time 98500.000       ->  frame   9860 time 98600.000       ->  frame   9870 time 98700.000       ->  frame   9880 time 98800.000       ->  frame   9890 time 98900.000       ->  frame   9900 time 99000.000       ->  frame   9910 time 99100.000       ->  frame   9920 time 99200.000       ->  frame   9930 time 99300.000       ->  frame   9940 time 99400.000       ->  frame   9950 time 99500.000       ->  frame   9960 time 99600.000       ->  frame   9970 time 99700.000       ->  frame   9980 time 99800.000       ->  frame   9990 time 99900.000      Reading frame   10000 time 100000.000    ->  frame  10000 time 100000.000      Last frame      10000 time 100000.000   
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "A university faculty is 500 egotists with a common parking problem." (Keith Sullivan)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 20: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 7 frames were processed by cpptraj for use in calculation.
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /home/romi/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Beginning PB calculations with /home/romi/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Parsing results to output files...

[WARNING] BOND component is reported as inconsistent. Please, check the output file for more details
[WARNING] BOND component is reported as inconsistent. Please, check the output file for more details
[DEBUG  ] Creating converter from 5 to 3
[INFO   ] Timing:
[INFO   ] Total GROMACS setup time:                   0.164 min.
[INFO   ] Total AMBER setup time:                     0.010 min.
[INFO   ] Creating trajectories with cpptraj:         0.005 min.
[INFO   ] Total calculation time:                    11.896 min.
[INFO   ] Total GB calculation time:                  1.746 min.
[INFO   ] Total PB calculation time:                 10.150 min.
[INFO   ] Statistics calculation & output writing:    0.003 min.
[INFO   ] Total time taken:                          12.079 min.

[INFO   ] 
   Finalizing gmx_MMPBSA: [ERROR  ] = 0; [WARNING] = 2
   Check the gmx_MMPBSA.log file for more details...

[INFO   ] 
 Thank you for using gmx_MMPBSA. Please consider supporting gmx_MMPBSA by citing our publication:
    Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. 
    gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. 
    J Chem Theory Comput., 2021, 17 (10):6281-6291. Epub 2021 Sep 29. PMID: 34586825.
    https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645

Also consider citing MMPBSA.py:
    Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E.
    MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
    J. Chem. Theory Comput., 2012, 8 (9) pp 3314-3321

[INFO   ] Opening gmx_MMPBSA_ana to analyze results...

[INFO   ] Finalized...
